Table 5.
Nucleotide and amino acid changes in the 3′ region of IBV CK/CH/LHLJ/04V and embryo-passaged derivatives.
| Gene | Position (nt)a | Nucleotide change |
Codon change |
Amino acid change |
|||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| P3 → P40 | P40 → P70 | P70 → P110 | P3 → P40 | P40 → P70 | P70 → P110 | P3 → P40 | P40 → P70 | P70 → P110 | |||
| S gene | 65–73 | ATTCTGATA (10/20)b | None | None | SDN | None (SDN) | None (SDN) | ||||
| 172 | None (A) | A → G (13/20) | A → G (14/20) | AGT → AAT | AAT → GAT | AAT → GAT | Ser → Asn | Asn → Asp | Asn → Asp | ||
| 173 | G → A | None (A) | None (A) | AGT → AAT | AAT → GAT | AAT → GAT | Ser → Asn | Asn → Asp | Asn → Asp | ||
| 194 | A → G | None (G) | None (G) | GAG → GGG | None (GGG) | None (GGG) | Glu → Gly | None (Gly) | None (Gly) | ||
| 397 | C → T | None (T) | None (T) | CAT → TAT | None (TAT) | None (TAT) | His → Tyr | None (Tyr) | None (Tyr) | ||
| 914 | A → G | None (G) | None (G) | TAT → TGT | None (TGT) | None (TGT) | Tyr → Cys | None (Cys) | None (Cys) | ||
| 1741 | None (C) | None (C) | C → T (12/20) | None (CTT) | None (CTT) | CTT → TTT | None (Leu) | None (Leu) | Leu → Phe | ||
| 2476 | None (G) | None (G) | G → T (15/20) | None (GAT) | None (GAT) | GAT → TAT | None (Asp) | None (Asp) | Asp → Tyr | ||
| 2503 | None (C) | None (C) | C → T (15/20) | None (CTT) | None (CTT) | CTT → TTT | None (Leu) | None (Leu) | Leu → Phe | ||
| 3088 | None (T) | None (T) | T → C (15/20) | None (TTT) | None (TTT) | TTT → CTT | None (Phe) | None (Phe) | Phe → Leu | ||
| 3469 | G → T (10/20) | G → T | None (T) | GAA → TAA | GAA → TAA | None (TAA) | Glu → #c | Glu → # | None (#) | ||
| Gene 3 | ORF 3a | Noned | |||||||||
| ORF 3b | 153 | None (G) | None (G) | G → T (12/20) | None (GAG) | None (GAG) | GAG → GAT | None (Glu) | None (Glu) | Glu → Asp | |
| ORF 3c (E) | 264 | C → T | None (T) | None (T) | AAC → AAT | None (AAT) | None (AAT) | None (Asn) | None (Asn) | None (Asn) | |
| M gene | 638 | None (A) | None (A) | A → C (10/20) | None (GAG) | None (GAG) | GAG → GCG | None (Glu) | None (Glu) | Glu → Ala | |
| Noncoding | 241e | None (C) | None (C) | C → T | NAf | ||||||
| Gene 5 | ORF 5a | Noned | |||||||||
| ORF 5b | Noned | ||||||||||
| N gene | 283–284 | None (TA) | None (TA) | TA → AC (13/20) | None (TAC) | None (TAC) | TAC → ACC | None (Tyr) | None (Tyr) | Tyr → The | |
a
The position of nucleotides from the AUG start codon of each gene ORF.
b
A 9-bp sequence, ATTCTGATA, was deleted in 10 out of 20 clones of CK/CH/LHLJ/04V P3, resulting in three deletions from amino acids 23–25 of S. The viruses P40, P70 and P110 do not have this deletion. Shown is the number of clones showing nucleotide mutations/number of clones sequenced.
c
#, stop codon.
d
No nucleotide mutations or amino acid substitutions were found in those ORFs between CK/CH/LHLJ/04V virus passages.
e
241 bp downstream of stop codon of M gene.
f
NA: not applicable.